Re: [Libmesh-users] Enabling netcdf4?

[David K. <dav...@ak...>]

On Wed, Aug 8, 2018 at 3:49 PM, Paul T. Bauman <ptb...@gm...> wrote:

> HDF5 is turned off by default, even with --enable-everything. You need to
> additionally feed --enabled-hdf5 to configure now.
>
> https://github.com/libMesh/libmesh/pull/1766
>
>
OK, but I'm having trouble getting configure to detect hdf5, even with
--enable-hdf5. I tried installing ubuntu packages for hdf5 but that
apparently didn't work, so I built it from source instead, but I'm not sure
if there's an option for specifying the location? Is
--with-hdf5=/path/to/hdf5 option? I don't really want to install into a
system directory in this case.

Do you use hdf5 with libMesh? If so, what is your approach?

Thanks,
David




> On Wed, Aug 8, 2018 at 3:31 PM David Knezevic <dav...@ak...>
> wrote:
>
>> On Wed, Aug 8, 2018 at 3:18 PM, David Knezevic <
>> dav...@ak...>
>> wrote:
>>
>> > On Wed, Aug 8, 2018 at 1:58 PM, Kirk, Benjamin (JSC-EG311) <
>> > ben...@na...> wrote:
>> >
>> >> netcdf-4 requires an underlying hdf5 library be found on your system;
>> was
>> >> that properly detected by ./configure?
>> >>
>> >
>> > Thanks, that's helpful! I just installed libhdf-5-dev in Ubuntu "apt-get
>> > install libhdf-5-dev") and now ./configure seems to detects netcdf-4,
>> > e.g. I get this output during configure:
>> >
>> > <<< Configuring library with NetCDF version 4 support >>>
>> > defining -DNOT_NETCDF4 for our Exodus build
>> >
>> > ...
>> >
>> > === configuring in contrib/netcdf/v4 (/home/dknez/software/libmesh_
>> > build/opt_real/contrib/netcdf/v4)
>> > configure: running /bin/bash /home/dknez/software/libmesh-
>> > src/contrib/netcdf/v4/configure --disable-option-checking
>> > '--prefix=/home/dknez/software/libmesh_install/opt_real/libmesh'
>> > '--enable-everything' '--enable-slepc' '--with-metis=PETSc'
>> > '--with-subdomain-id-bytes=4' '--with-boundary-id-bytes=4'
>> '--disable-glpk'
>> > '--enable-unique-id' '--with-unique-id-bytes=4'
>> '--with-nlopt-include=/home/
>> > dknez/software/libmesh_install/nlopt/include'
>> > '--with-nlopt-lib=/home/dknez/software/libmesh_install/nlopt/lib'
>> > '--with-capnproto=/home/dknez/software/libmesh_install/capnp'
>> > '--disable-parmetis' '--disable-ifem' '--with-methods=opt'
>> > '--enable-shared' '--disable-netcdf-4' '--disable-testsets' 'CXX=mpicxx'
>> > 'CC=mpicc' 'F77=mpif77' 'FC=mpif90' 'CPPFLAGS= ' 'LIBS= -ldl '
>> > --cache-file=/dev/null --srcdir=/home/dknez/software/
>> > libmesh-src/contrib/netcdf/v4
>> > configure: netCDF 4.4.1.1
>> >
>> > ...
>> >
>> > Optional Packages:
>> >   boost............................ : yes
>> >   capnproto........................ : yes
>> >   cppunit.......................... : yes
>> >   curl............................. : no
>> >   eigen............................ : yes
>> >   exodus........................... : yes
>> >      version....................... : v5.22
>> >   fparser.......................... : yes
>> >      build from version............ : release
>> >   glpk............................. : no
>> >   gmv.............................. : yes
>> >   gzstream......................... : yes
>> >   hdf5............................. : no
>> >   laspack.......................... : no
>> >   libhilbert....................... : yes
>> >   metis............................ : yes
>> >   mpi.............................. : yes
>> >   nanoflann........................ : yes
>> >   nemesis.......................... : yes
>> >      version....................... : v5.22
>> >   netcdf........................... : yes
>> >      version....................... : 4
>> >   nlopt............................ : yes
>> >   parmetis......................... : no
>> >   petsc............................ : no
>> >   qhull............................ : yes
>> >   sfcurves......................... : no
>> >   slepc............................ : no
>> >   thread model..................... : pthread
>> >   c++ rtti ........................ : yes
>> >   tecio............................ : no
>> >   tecplot...(vendor binaries)...... : no
>> >   tetgen........................... : no
>> >   triangle......................... : no
>> >   trilinos......................... : no
>> >   vtk.............................. : no
>> >
>> >
>> > However, I then tried to read the same netcdf-4 ExodusII file, and I
>> still
>> > get the same error as before. So I guess ExodusII hasn't been configured
>> > with netcdf-4 after all? The line "defining -DNOT_NETCDF4 for our Exodus
>> > build" in the configure output seems to suggest that exodus is not using
>> > netcdf-4, which would explain my issue, do you know what I should do to
>> > resolve this?
>> >
>>
>>
>> I gather that the issue is that my hdf5 build is not being detected by
>> ./configure properly after all, since I have
>> "hdf5.............................
>> : no:. I'll try installing hdf5 from source and see if that fixes it.
>>
>> David
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